5LI7

Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with 1-(3-(1H-imidazol-1-yl)propyl)-3-((3s,5s,7s)-adamantan-1-yl)urea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OXA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2M sodium sulphate, 0.1 M Hepes pH 7.5 and 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.25α = 90
b = 69.91β = 90
c = 226.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2011-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5857.3199.80.02420.17.3122489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.621000.8292.65.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1OXA1.5857.3112248864861000.171760.17010.20327RANDOM16.426
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.110.24-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.535
r_dihedral_angle_4_deg17.701
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg5.748
r_scangle_it5.353
r_scbond_it3.404
r_mcangle_it2.26
r_angle_refined_deg2.056
r_mcbond_it1.333
r_angle_other_deg1.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.535
r_dihedral_angle_4_deg17.701
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg5.748
r_scangle_it5.353
r_scbond_it3.404
r_mcangle_it2.26
r_angle_refined_deg2.056
r_mcbond_it1.333
r_angle_other_deg1.124
r_mcbond_other0.443
r_chiral_restr0.139
r_bond_refined_d0.027
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5881
Nucleic Acid Atoms
Solvent Atoms998
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling